Possession
by Wesfan1234
Summary: John plans the ultimate rescue, only to mess it up royally. Will he ever see Atlantis again? Spoilers for S5 Ghost in the Machine.
1. Chapter 1

Title: Possession

TV Show: Stargate Atlantis

Rating: K+ right now. I don't know what it'll be in the future.

Pairing(s): John/Elizabeth, slight John/Fran if you look for it

Disclaimer: If I'd owned this, John and Elizabeth would have been together. But I don't. And I'm definitely not making any money off of this.

Summary: John plans the ultimate rescue, only to mess it up royally. Will he ever see Atlantis again?

Notes: I'm doing this on the fly, which means it'll be a WIP until it's done. I sort of have it mapped out, but who knows where it'll go. I just so want to get back into writing again. Good reading! Enjoy. Comments are very welcome.

**Chapter One**

Pins and needles. His arm had fallen asleep, making him want to shake it until he got the feeling back in it. What he didn't count on was the sharp pain in his shoulder as he eased off of it.

"You seem to be injured."

Statement of the century. John Sheppard always seemed to be injured in some way. Mostly cuts and bruises, but sometimes he came back with concussions, broken arms, legs, burns. Once he even came back through the gate with an arrow in his hip. Elizabeth never ran so fast to try and catch him as he stumbled. John moved his arm purposely just to get that image out of his head. Pain was a good way to forget.

"Dammit. I do not need this."

No, he didn't need to be injured, out in the middle of nowhere, no team, no way back to Atlantis. What started out as a carefully planned operation turned into a disaster. On top of ruining his career, he now had ruined his chance of ever seeing Atlantis again.

"Shall I help you?"

If he could slam her against the bulkhead, he would. But he needed Fran, possibly to survive.

"I'm fine," he growled, while edging himself up to the bench in the back of the puddlejumper.

"You do not seem pleased. If I have done you any harm, I am truly sorry."

Harm? All she did was somehow delete everything he had worked for these past couple of months. She was back at factory settings, unfortunately. Rodney would be proud.

John's head swam as he leaned back against the bulkhead. What would he do now? Find a decent planet to land on, possibly with a Stargate? Not that he could actually dial back to Atlantis. Woolsey probably already deleted his IDC from the computer. Slamming into the shield wasn't his idea of fun.

Levering himself against the bench, John slowly made it to a standing position. His arm hurt like hell, his head hurt worse than hell and the rest of his body felt like it had gone ten rounds with Ronon. Oh boy, Ronon was probably pissed off right about now. He could see in his mind Teyla's face, disapproving of a plan that really didn't have any room for success. Suicide mission at its finest. John Sheppard seemed to excel at those.

"Would you like me to…," Fran started until John put a hand out for her to shut the hell up.

"Listen, just sit down and shut up."

"As you wish," Fran replied, sitting across from him. John thought he heard a little hurt in her voice. What emotions had Rodney programmed into her?

Rodney hadn't entirely programmed this model though. Elizabeth had. With all her Replicator knowledge on top of the knowledge that Rodney had managed to glean in making Fran in the first place, this was one lean, mean machine standing in front of him. Not that he was worried. Why should he be? He was screwed anyway.

Making his way to the front of the puddlejumper, John slid into the pilot's seat to figure out just where in hell they were. Blackness, a few stars off in the distance. No way to make out anything of importance. John tried to call up the display of wherever they were. It didn't work.

"While you were unconscious, I tried to accomplish that task also. It seems that many of the ship's systems are not communicating with one another."

"Polite way of saying that it's all shot to hell. Kind of figured that out."

It bothered him the way she sat next to him, like she belonged there.

"I do not believe that the systems are all shot to hell," Fran replied, saying his wording hesitantly. "They are just not communicating properly."

"Get to the point. You know how to fix it or not?" He knew he sounded a little annoyed. Who wouldn't be, trapped in a part of the Pegasus Galaxy he'd never been to, retrieving what he thought would be Elizabeth Weir, only to come up short, again.

"I think it would be possible. Would you like me to?"

John snickered at that thought. Hey, he could just open the rear hatch and end it quickly. He was never one to think those kinds of thoughts though. He'd fight to the last breath if he thought he'd be able to live.

"Have at it. I'm not going to get much done with this arm and the pounding headache," he said as he raised his battered body from the pilot's seat.

Fran got to work as he rummaged around to find the medkit in the back. Blessedly, it was packed to the gills with medicine, particularly some pain killers and a way for him to bind his arm to his body so he wouldn't move it. He just couldn't wrap the damn thing up without help. After trying a dozen times, he finally called to Fran to help.

She gently did as she was told, even giving him a slight smile when she finished. John only downed one pill, just to take the edge off, but not to put him off in lala land, as pain meds sometimes did to him. Four hours later (he checked how long he'd been out), he saw that Fran was making progress. Good for her. Thank goodness she still had Rodney's programming intact.

"There are certain systems that I cannot operate because I do not possess the Ancient gene. When I have completed repairs, I will need your help." She looked so pleased with herself.

John puttered around, tried to not be in the way, ate a powerbar, then attempted to help. Fran frowned at him. At least Rodney didn't program sarcasm. He figured that sitting down and staying out of the way was the best course of action. The pain was bearable at the moment. Moving around too much might make it worse. He settled down in the co-pilot's chair because that seemed to be the only place Fran hadn't been working.

* * *

"I never thought of you as a wimp," the voice taunted as it ran ahead of him.

"Nah. Not a wimp. Just ask Ronon or Teyla. Don't ask Rodney," he put in as he followed the voice through Atlantis.

It all seemed so familiar. The banter, the easiness with which they talked. When he finally caught up with her, he noticed she was sweating. He was too. They were running. He and Elizabeth were running. John didn't remember a time when she joined him in a run around Atlantis. Hell, even Rodney had joined him once, never to do it again. He had to take Rodney to Carson after that incident.

"Why are we running?" he asked Elizabeth.

"Because you wanted to. You explained that it cleared your mind."

John watched as Elizabeth wiped her face with the back of her hand. The only time he'd seen her sweat was when she was seriously injured.

"You OK?" he suddenly asked, realizing that taking her running wasn't the best idea.

"Just a little winded. It's beautiful here, isn't it?"

He couldn't agree more. John usually ended up on this lonely little deck far away from Atlantis's inhabitants after a long run. All he could see was ocean as far as the eye could see. That suited him just fine. And to share it with Elizabeth, that was even better. She never had down time, to relax and enjoy the city as she should.

He watched as she took a deep breath. Staring at her didn't make her wary as it did when they first met. He had a habit of just looking at her, trying to figure out the puzzle that was Elizabeth Weir. Some people thought they had something going on, at least to the level of a weird kind of ESP. He sometimes wondered about that too. They definitely had some kind of connection or maybe he was just good at reading her facial expressions.

"What?" she asked as she turned to meet his stare.

"Oh, just the fact that you are actually relaxing at the moment. You never seem to do that."

"And your idea of relaxing is running a few miles, sparring with two people with many times the strength of yourself, then raiding the kitchen for the leftover ice cream from the night before?"

John just couldn't help but smile. "You really do know me. I'm a simple man. If I don't get the ice cream, then Rodney will find it and eat it before I do."

Elizabeth smirked at that thought. "So it's a game between the two of you?"

"No. I just like to piss him off."

Elizabeth Weir actually snorted. Her shoulders weren't bunched up with tension, her brow wasn't furrowed with worry, her stance wasn't one of being ready to fight. He'd actually gotten through to her.

* * *

The jolt of the puddlejumper moving woke him from his slumber. John's good hand rested on the controls in front of him, looking as if they were lighting up from his touch. Which meant one thing: Fran was successful. Now they could roam the galaxy, orphans from their respective races.

"I did it," Fran exclaimed, a little excited that she was able to repair the shuttle.

"You did," John mumbled as he moved from one chair to another. "Wild blue yonder, here we come."


	2. Chapter 2

Yeah. Chapter two is up and running. Reviews anyone? I don't bite. Any time you want to review! Or just wave to say hi and that you're reading. I know this is a new fandom for me. I do hope you're enjoying this so far. It's still rated K+ for now. I'll change the rating if necessary. Thanks for reading. Chapter three will be on its way in a few days.

**Chapter Two**

"Don't you fucking dare touch that."

They all had it wrong. No way Sheppard would ever abandon them. Even Teyla had to be wrong, although it didn't happen often. Ronon slammed his fist down next to the controls of the stargate.

"Ronon, you have to understand that this is necessary. If Colonel Sheppard has been compromised, then we need to take all precautions to protect the city and its inhabitants."

Woolsey sometimes really pissed him off. Just because he was right didn't make Ronon feel any better about it. Sheppard had to have his reasons. If he didn't get an answer when he found the son of a bitch, then he'd make sure to beat it out of him. Why did the man have to be so stubborn?

"I'm not done looking for him. I've triangulated the last known location from where the puddlejumper gated to. If you just give me a couple of hours, I'll be able to get you a gate address and we can go after his sorry ass."

Rodney always had a way with words. Ronon was going to kick his ass, sorry or not. Teyla stood beside him, if just to hold him back if need be.

"You do your calculations, McKay. It still doesn't change the fact that Colonel Sheppard abandoned his post. He is AWOL as of now. Now if you'll excuse me, I need to check on the Marine that Sheppard decked."

It was just a scratch, Ronon thought. Wimps, all the Marines were. Of course, with Lorne standing on the other side of him, he didn't want to voice that particular comment. He didn't feel like taking Lorne down at that moment.

"Chuck, if any, I mean anyone dials into that gate, I'm to be notified immediately," Rodney insisted, pointing to the man in charge of the gate.

"Yes, sir." Ronon thought that Chuck almost saluted.

Ronon watched as Rodney hurried off to figure out where in hell Sheppard was. The mutterings that Rodney was engaged in with Zelenka weren't very nice. Something about stupid idiot and why didn't he tell me were part of the conversation.

Yeah, why didn't Sheppard tell anyone he had a plan? Well, maybe because Sheppard's plan was a piece of shit, that was why. And probably because he didn't want to get anyone else in trouble if it went wrong. It did go wrong, from what they found.

He, Teyla, Rodney and Lorne gated to the address that Sheppard had traveled to a few hours before. There was nothing left but debris from something very big, possibly a ship. Certainly was too much junk for it to be a puddlejumper. There had been a battle, a very big battle in the middle of space. Sheppard possibly had gotten caught up in it. Yeah, he possibly was in that debris.

Rodney didn't detect any Ancient machinery though. That was a good sign. The gate had been activated many times in those few hours that Sheppard had disappeared. None of the gate addresses were ones they had on file.

By the time they made it back to Atlantis, Woolsey was chomping at the bit to flay Sheppard alive. Seems that Sheppard took out a Marine to take a puddlejumper. What the hell was the man thinking?

He could think of a few choice statements, but the one that best described John Sheppard was loyalty. Never leave a man behind. That motto was something that the Satedan could live by. Each time one of them was left behind, whether it was Teyla being kidnapped by Michael or himself getting messed up with his former buddies, Sheppard was always there to find them. He didn't give up.

So Ronon wouldn't give up. He damn well knew that Rodney wouldn't give up. Teyla looked fierce and determined standing next to him. Lorne was a Marine, so that was a given. They'd find the bastard.

"I am so kicking his ass when we find him," Ronon said aloud.

He heard Lorne snort as he watched that twinkle in Teyla's eyes. He wouldn't have to do the ass-kicking himself. Teyla would take care of that for him.

* * *

John couldn't get his bearings. Nothing was familiar in this star system. It seemed like they'd been flying around for hours, no progress. They scanned for a stargate, but no luck. Pretty soon, they'd have to find an inhabitable planet. He couldn't live on powerbars alone, unlike Rodney.

The pain meds had worn off, but he was gritting his teeth against the pain. Luckily the puddlejumper was flying smoothly since Fran had fixed it. Every once in a while it would jerk. Inertial dampers must not be calibrated correctly, he thought. They were airborne though. That's what counted.

"We need to find a place to set her down," John announced.

"A suitable place to sustain human life," Fran offered back.

They hit a bump in the road, causing John to groan in pain again. One more of those, he'd definitely have to dig into the medkit.

"There were three planets that could sustain life not far from our position."

John was glad that Fran could take the information that the displays were giving her and process it all. All the information on the screen had started to dance before his eyes.

"Whichever one's the best."

As he turned to look at Fran, he noticed that she had started to waver before his eyes. Crap, he thought. I can't lose consciousness now. Who would fly the jumper? Just before he slumped over, he told the jumper to fly on autopilot, hopefully to get them down on the nearest planet. He hoped it was enough. Otherwise, they'd be stuck until whenever.

* * *

"How do you do that?"

Do what? What was he doing? Opening his eyes, he was sitting in Elizabeth's office, in the chair that he always occupied when they had meetings. His arms were crossed, his feet stretched out in front of him. And his neck hurt just a little.

"What?"

"Sleep with all this activity going on around you. I thought you were going to fall out of the chair there for a moment," Elizabeth told him with that smirk she was famous for on her face.

"You would have woken me up before, wouldn't you?"

"Maybe," she replied, drawing out the word like she didn't really mean it.

He couldn't exactly remember why he was in her office. It must have been a long day for him to fall asleep right in front of her.

"Go find your bed. I'll finish this up." Elizabeth rose to shoo him out of her office.

"I'll wait. You're almost done, right?"

Elizabeth rolled her head around like she'd been sitting there for a while. The dark circles under her eyes told him that she'd been up too many hours without rest. It was surprising that she didn't just fall asleep in her chair also.

"As done as I can be. Shall we?" She gestured for the both of them to leave.

As John walked her to her quarters, he contemplated asking her for a late night snack in the kitchen. As he watched the weariness in her steps as she walked, he knew that she just needed rest. He'd make sure in the morning that she had a good breakfast, even if he had to bring it to her and force feed it.

Stopping outside her quarters, Elizabeth turned, tilting her head just slightly.

"I should," Elizabeth started.

"Yeah, so should I. Don't you dare go in there and read reports or something," he admonished her.

"Me? I'd never do that."

He knew her too well. She so would.

As he turned to go, her arm touched his, making him stop in his tracks. "It's not your fault. You did everything you could. Please don't blame yourself."

Blame? Here they were, having an evening stroll. He thought that they had both just been working too hard and needed rest.

"My mind's a little fuzzy. What were we talking about?"

Her hand still touched him. Even through his jacket, he could feel her warmth.

"It's not easy to deal with," she continued.

Now he was clueless. What had happened that day?

"Deal with? I'm just not remembering the details very clearly." Maybe he should go see Carson before hitting the sack.

"Not rescuing me," Elizabeth shouted back.

* * *

Hope you enjoyed! Thanks for reading.


	3. Chapter 3

Author note: Thanks for the reviews so far. Shout out if you're reading. I'm having fun doing this. I hope you're having fun reading.

Author note 2: I'm not working with a beta on this so all mistakes are mine. Still rated K+ for the moment

Enjoy!

**Chapter Three**

The pain was now unbearable. He usually wasn't one to scream, but he did. He'd been thrown against the front console of the puddlejumper. Had they crashed? The interior of the jumper wasn't exactly lit up very well at the moment. His chest was burning, like maybe a rib was broken. Just what he needed.

"You must not move," Fran stated, hesitating between each word.

What in hell was going on? Just as he turned his head, he noticed that Fran was standing right beside him. Holy shit, she had some kind of pipe stuck straight through her. There was nothing he could do about it. Each movement, each muscle that he tried to move hurt like hell.

"I must rest. Shut down for repairs." Dammit, it sounded like she was gasping for breath. Replicators don't breathe. She fell back, out of his line of vision, with a resounding thud.

John closed his eyes for a moment, to gather his strength. If Fran was down, who would do the repairs? He had to think of what to do next. If he could get to the medkit, he could possibly bind his ribs enough to move around. Each breath he took though taxed his strength. He could still breathe, so the lung wasn't punctured. He was alive, for now.

* * *

"You are not dying on me now," John shouted as Carson worked on Elizabeth.

The explosion had torn up half the control tower. They were lucky they hadn't lost the stargate. But they had lost something: their leader. There was no way they could survive the next attack without Elizabeth Weir at the helm. No way.

John tuned out Rodney's constant chattering on his headset, only focusing on saving Elizabeth. He waved away a nurse who had come to bandage his own wounds until Carson had ordered him to sit down before he fell down. Damn doctors.

John sat day and night with her, or had someone else sit with her if he was needed. Since John couldn't really do anything about repairing the station, he could sit for the most part. In his mind he was already planning on how to beef up the security systems. Writing it all down on a spare laptop he had Radek deliver, John knew that by the time Elizabeth woke up from surgery he would have a working plan in place, one that would protect the city and her.

What he didn't count on were the setbacks in Elizabeth's condition. They even thought at one point they might lose her. That's when he took her hand and literally willed her to live. Laptop forgotten, plan forgotten, everyone else forgotten but Elizabeth Weir and willing her to live.

Exhausted, John thought he'd just catch a short nap by laying his head on Elizabeth's bed so he wouldn't be away from her. He thought he was dreaming when he felt fingers comb through his disgusting hair. Carson had made him clean up after the explosion, but not since then. He was surprised that none of the nurses had demanded for him to have a sponge bath, or at least be hosed down.

Sighing, he repositioned his head. The little moan he heard beside him made him sit up and take notice of what was really going on. It was indeed Elizabeth's hand that had been stroking him.

"Elizabeth?"

Her eyes opened ever so slowly, a little smile spreading across her face.

"You in there?"

"Yeah," she whispered. "You stink."

John laughed like he never had before.

* * *

Teyla was more worried than she had ever been about John. He must have been planning to rescue Elizabeth for quite some time, Teyla surmised. She knew he hadn't intended on injuring one of his fellow warriors, but it happened. She agreed with Mr. Woolsey that John was in trouble. Of course, for other reasons, one of which was not including her in on the planning of this rescue mission.

Elizabeth had been like a sister to her, slowly letting Teyla into her life over the course of their friendship. She also knew there was much more to John's relationship with Elizabeth than met the eye, as the Earth saying went. John Sheppard was just as stubborn as Elizabeth was.

Teyla assisted Rodney in any way she knew how, which was not much unfortunately. Bringing him coffee when needed and providing encouragement was all she could provide to the search. None of the addresses Rodney had obtained from the spacegate that John had used on the other side proved to help them. John must have gated to another gate after encountering the trouble. They had tried gating back to the spacegate they had first traveled to, but they could not establish a link.

Rodney had explained to her that it had possibly been destroyed by some of the floating space debris or maybe the battle had resumed after they had left. Since there was evidence of more ships in the vicinity, she voted for the later. She just hoped that John had not been captured by one of their enemies.

Lorne and Ronon had gone on a fact-finding mission, trying to find any information about the battle they had encountered and to ask any of their sources if John had been captured. Nothing had been reported so far.

Teyla hated waiting. It wasn't something in which she was skilled. She could fight, protect her people, keep them as safe as could be, but waiting wasn't a skill she had acquired.

Rodney kept up his work, fueled by food and coffee. At one point, he would need rest. After showing her several possible gate addresses, they added those to the ever-growing list to send a team to investigate. It was when Rodney had given her the same set of addresses that she put a stop to his research.

"Rodney, you need rest."

Rodney rubbed a hand across his face. "I'm fine, really, I'm fine."

"You do not seem to be fine. You gave me these addresses two hours ago."

"This is just, I'm just…" Rodney related to her.

"Frustrated beyond words, as am I. But you need a fresh mind. If you do not get enough rest, you will collapse."

Rodney shook his head in agreement. "Yeah, you too."

She wouldn't rest though. Checking in on Torrin, Teyla meditated for a short while and then made her way to the control room. She could not rest until there was word from the others. John Sheppard had not given up on her when Michael had kidnapped her. She would not give up on him, ever.

* * *

It's drafty in here. Someone must have opened the hatch. Shit, John thought, sitting up so fast he thought his head would fall off. No, they weren't floating in the vacuum of space. It was actually quite warm and humid. And his shirt had disappeared only to be replaced by lots and lots of bandages. Hey, he could breathe better. Not perfectly done bandages, but it worked. He was able to get up without a tremendous amount of pain.

"Drugs. Can't live without them," he muttered to himself as he looked around for any sign of Fran.

Well, they landed somewhere. This somewhere had an atmosphere that supported human life. The jumper looked to be in one piece, not working but in one piece. But no Fran. Could she have bugged out, not wanting to help him?

John had no sense of time. How long had he been unconscious? His stomach rumbled as he looked at his watch, which was now cracked. The story of his life. Takes a licking, but keeps on ticking.

Searching for his shirt, John explored the front of the jumper, still not finding Fran. No shirt either. The consoles in the front were still warm to the touch, either from use or the humid weather. Maybe there was a possibility that power could be restored. As he ran his hand across the board to get anything, he felt a little electrical charge as he did.

"That's new," he said to no one.

* * *

"No, it's not. I've worn this before," Elizabeth said as she and John sat down in the mess hall. "Don't you remember?"

John ran his hand over the surface of the table. It was smooth, cool to the touch. Wasn't he just running his hand over a console in a jumper?

"No. Not sure that I do. What were we talking about?"

The mess hall's lighting was subdued, possibly due to the fact that it was late evening. He and Elizabeth often had late dinners together or at least a snack before turning in for the night, if just to catch up on their respective days.

"You were worried. John, is everything alright?"

"Yeah. Peachy."

It was humid. It was never humid in Atlantis, except for the time that Kolya had taken over. That was ages ago, a time that John would rather forget. Bastard had tried to kill Elizabeth.

"Is it humid in here? Maybe I should have Rodney look at the temperature controls?"

Elizabeth stuck her hand out to feel his forehead. Oh geez, she thought he was running a fever.

"You do feel a little warm," she told him as she withdrew her hand abruptly.

"It's just the humidity is bothering me." That wasn't the only thing that was bothering him. Something wasn't right. He reached his hand out, now noticing what was strange.

"My shirt," he said as his hand touched her arm.

* * *

Fran was wearing his shirt. Why was she wearing his shirt?

"You are awake." She was standing way too close for comfort, especially after that little dream episode of his.

"Am I? Why are you wearing my shirt?"

Fran quickly got away from him, but he caught up with her before she could exit the jumper. Turning her around to face him, he took both her arms into his hands, just to make sure she didn't get away from him.

"What's going on? Just answer my question, dammit."

Fran tried twisting away from his grip, but he was still surprisingly strong.

John had rarely been rough with any woman of any kind. Teyla could still kick his ass and he wouldn't, couldn't ever hurt her. But this wasn't a woman standing in front of him, it was a machine. He didn't know why the shirt meant anything to him. It was so warm, he really didn't need it anyway. It was the thought that Fran took it from him without his permission.

"It's mine. Give it back," he demanded and she complied, but not before turning around.

Before John could say what she threw it to him, covering herself. His gasp made her flinch. She was naked from the waist up, back to him, large gaping hole square in the middle. It looked to be slowly healing, he thought.

"I'm sorry," he started. "I didn't mean to make you uncomfortable."

Dammit, she was a machine, not a person. Here she was acting like a person, a human being with feelings, insecurities. He placed the shirt back over her shoulder, turning around, attempting to gather his thoughts at this latest development. What popped into his mind next was something he'd wanted to know but hadn't had time to ask?

Her quick explanation after he had retrieved her from the vacuum of space hadn't settled his mind in the least.

"What happened? Where is she?" he asked as he turned back to face Fran.

Fran had put his shirt back on. She took a few steps backward, like she just might run. Was she afraid of him? Her hair was damp and curly from the rain and humidity of the planet they had landed on. Just like…

He had it. Fran knew he'd had it. She stumbled out of the jumper, falling to the ground outside. A bolt of electricity arched out and hit him square on the thigh, sending him crashing to the deck.

* * *

"Don't touch her," Elizabeth warned.

The two of them were in the gateroom, no one else around.

"There's no one else here, Elizabeth. By the way, where is everyone?"

This gateroom seemed cold, uninhabited, much like it was when they first stepped onto Atlantis, which was a lifetime ago for the both of them.

"I'm not touching anyone." John's thigh hurt. He rubbed the sore spot while Elizabeth circled him.

"It's not her fault. Just listen to me."

Her? Fran. Had to be. But they were on the jumper on a humid planet.

"I'm not here, am I?" John's thoughts started to clear somewhat.

"No. You're not. I don't have much time. This will only last a few minutes. Just trust me on this. Fran is not your enemy."

John almost asked if Elizabeth was, but he knew she wouldn't answer that one for the moment. He wanted her to get to the point.

"One, I'm injured, landed on a planet in the middle of nowhere, and now I'm hallucinating. Am I getting close?"

Elizabeth stopped circling him, her eyes pleading with him to think. "No. I mean you're not hallucinating. Just listen to me. She's scared. Her programming is breaking down. You've got to help her."

Oh, so that was it. Fran was falling apart and he had to fix her. Ha, that wasn't likely to happen.

Elizabeth approached him, standing close to him. It wasn't like she was invading his personal space. She always seemed to invade his personal space on Atlantis; a hand brush here, a foot there, a look at any time. Just like they were connected at the hip. The hand on his cheek sent another bolt of energy through his body, making him fall to his knees.

* * *

"Stop doing that, OK," he announced to the air.

Fran had stopped her struggles and was sitting up in the rain and mud, drenched to the bone. Crap. He did not need this. A machine that was afraid of him, a puddlejumper possessed by his former boss and his mind going into overload. He needed to sit down. John's knees ached to just park on the ground, not to get up for a week.

"Fran, come back in. I'm not angry with you. Please."


	4. Chapter 4

Back from a weekend of camping. Chapter four is up and running. Thanks to all who have looked and read. Please comment. I hope there's not too much Sheppard whumping for anyone. Enjoy and keep reading.

**Chapter Four**

No, John was actually angry with Rodney. He had designed Fran to be the way she was. She was beautiful, knowledgeable, and usually had the strength of ten men. This was not the Fran that Rodney had created. What could be going so wrong with the programming that she would deteriorate? The vacuum of space could have played havoc with her systems, for one.

Dammit, they were both drenched now in addition to being up shit's creek without a paddle.

"Inside," John commanded, hoping that he'd pull himself together.

"You are angry," Fran started as they finally got out of the rain.

"It's just I don't know what's going on. What's wrong with your programming?"

Fran's head twitched back and forth. Her mouth moved, like she wanted to say something but couldn't. He needed her to get off this planet.

"You don't know?" he asked quietly.

She shook her head no in return. "Thoughts jumbled. Emotions jumbled. It hurts."

Her face grimaced as she struggled with the words. He really was going to kill Rodney when he saw him next.

"Is there something I can do?" As much as it pained him, he didn't want to see her suffer.

Her movements were jerky now, so he didn't think she would attack him. As she fumbled toward him, he thought he could handle it if she got physical. Her hands on his face, cold to the touch, startled him. This was definitely not what he was expecting. Her lips tasted like metal.

* * *

"This one," Rodney stated as he turned to look at Woolsey.

He better be right. They'd gated to too many damn places in the last few days, many of which were not habitable. If Sheppard had accidentally gated to any of these, he'd be dead. The man had nine lives, so Rodney was almost sure that they'd find him. Almost.

"The resources we're using to track Colonel Sheppard could be put to better use."

So could the use of Rodney's time and he wasn't complaining. He was just as angry with Sheppard as everyone else was, even more so. Any kind of plan, he should have been in on from the very beginning.

That bad feeling in the pit of his stomach wouldn't go away. No matter what happened, no matter if they found Sheppard or not, the man was screwed every which way to Sunday. The military would send him back to Earth, probably discharge him, possibly jail him, and most definitely see to it that he never, ever was able to travel to Atlantis again.

"Yeah, well, he screwed up. Again. What's going to happen to him, when we find him?" Rodney inquired as he tried to stay awake.

Woolsey looked too serious for his own good, Rodney thought. He leaned against the counter in Rodney's lab, and sighed.

"Dishonorably discharged, jail time. I'm not exactly sure. Let's just say it will not be pleasant once I report this to his superiors."

Bingo. Rodney had an idea. Richard Woolsey was going to save the day. Well, save Sheppard's sorry ass. That would be good enough.

"Did I ever tell you about the time…"

* * *

John's head hurt. He didn't remember how he'd ended up seated at the front console. He just remembered standing at the back of the puddlejumper, dripping wet from the rainstorm that now had turned into a monsoon. Then the world turned over and over in his head. He was hallucinating. That was it.

"You know what you have to do."

"I can't."

It was as simple as that. The risks were too great. He'd figure out another way. If Fran deteriorated too much, there would be no saving anyone. She was wrong. He knew it.

"If we don't fix her, neither one of us will get out of this."

Elizabeth was right. He knew that. Maybe he didn't want to get out of this mess. He was screwed no matter what he did. John stood in Elizabeth's office. It was decorated exactly as she left it, before the explosion, before the Replicators took control of her and damned him for life.

"If we do this, we may never get you back."

He was right about this too. She had jumped from Fran's frozen solid body as soon as he had retrieved it from the vacuum of space. Elizabeth was definitely better at communicating this time around than last time. Last time she almost brought the city down by just typing a few messages.

"I'm willing to take that risk."

Stubborn as always. She stood behind her desk, arms crossed in front of her, looking defiant as ever. It had saved their asses on many occasions.

The desk separated them. John had wanted it that way, had projected that thought before trying to contact Elizabeth again. He didn't want to be distracted by her. But even looking at her was distracting. Elizabeth leaned against her desk, arms propping her up, look of determination on her face. How many times had he seen her look exactly like that?

He moved within inches of her, mirroring her posture, just like old times. John liked sparring with her, liked seeing her get riled up.

"John, do you remember when I said that you needed to obey my orders?"

Yeah, and look where that got him. He abandoned her. Not again. Abandoning her was not an option this time. He'd die trying to save her. Ronon wouldn't be here to pull him away. Rodney wouldn't be around to save them at the last second. Teyla wouldn't be able to talk sense to him, to make sure he wasn't making the mistake of his life.

"I do."

This conversation wasn't going his way.

"This definitely is one of those times."

John snorted. Elizabeth really could be funny, when she wanted to be.

"You're not the boss of me," he shot back, knowing full well he was starting a fight at the worst time.

"What?"

"You heard me. I'll do whatever I damn well please."

Elizabeth snorted in return. This argument wasn't working.

"You will listen to me."

"Nope."

The metal taste went away, at last. Maybe he was dreaming when Fran placed her cold lips against his. There didn't seem to be any point in it. There definitely was a point to Elizabeth doing the same thing though. Definitely.

The desk still separated them. John locked his elbows, hoping that he didn't fall down flat on his face before actually touching Elizabeth Weir again. Even if this wasn't real, it sure seemed real for the time that he spent with her.

This was always his dream. He'd argue with Elizabeth, somehow piss her off, they'd go toe-to-toe, get face-to-face and both would lose it entirely. Nothing touched other than their lips.

Elizabeth stopped when she couldn't breathe anymore. The panting against his cheek warned him that he didn't have any more arguments left in him.

"If Fran fails, what happens to you?"

* * *

John touched the console in front of him. Sparks shot out, barely missing his head.

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	5. Chapter 5

Wow, thanks for all the reviews so far. Everyone reading and commenting has been terrific. Here's another chapter. Read and enjoy!

**Chapter Five**

"Ouch," John yelled for what seemed like the millionth time.

Elizabeth hadn't told him that the whole jumper was going to light up like a Christmas tree, with sparks flying everywhere. His hair smelled like it was burned, his eyebrows probably not there anymore, he couldn't feel his feet. This had better work, he thought.

As the smoke cleared in the jumper, he also wondered if they'd be able to repair all the damage that had been done to it. After this last round, he had some doubts about that. Plenty of doubts. But thank goodness Fran hadn't picked an ice planet to land. Freezing his ass off wouldn't have been so much fun at the moment.

The feeling in his feet returned with a vengeance, just as he was trying to stand up. John wasn't walking on pins and needles, kind of like what you'd feel if your foot fell asleep for a while. No, it felt like there was a burning hatchet in his foot that wasn't going anywhere anytime soon. He guessed that beat not being able to move at all.

Walking to the back of the jumper, he literally jumped off his feet as Fran appeared directly in front of him. It was almost like she was a zombie. He'd better lay off showing Ronon those movies for a while, if he ever saw Ronon again.

Fran didn't speak to him but went straight to work. He never saw Rodney work this fast, even when their lives were in danger and there was three minutes until their destruction.

Every time he tried to help, Fran pushed him out of the way. So John did what he did best: he patroled the perimeter, just to make sure there wasn't anyone else lurking around to make their lives miserable. From time to time, he peeked in to see what progress she had made. Once or twice she even waved him over to try something on one of the panels. No juice yet.

Fran did complain when he decided enough was enough and he needed to rest. Only she did so with the silent treatment. If looks could kill, he'd be mashed up into tiny bits on the floor at that moment. He was tired, sore and more than just a little hungry. With only a few power bars left, he broke one in two and offered the other part to his possible savior.

"I do not need to eat," she finally spoke aloud.

"Just checking. Look, I need to rest. Don't you ever rest?"

John slid to the floor at the back of the jumper, stretching his legs out. He might not ever get off the floor again as he realized that everything hurt. Well, almost everything. It was possible that his pinky might not hurt too badly.

"I do not need to sleep, if you must know. I will continue with the repairs as necessary."

Then she walked away, not wanting to chit chat with the broken human on the floor that was scattered with bits and pieces of his damn jumper. The thought that Elizabeth was in there somewhere, propping her up to get the job done made him a little crazy inside. He wanted Elizabeth safe and sound, not inhabiting a dying robot. He didn't know what else to call Fran.

"John Sheppard," Fran called from the front console, "I need your assistance with this console."

She needed his ancient gene. He bet if there had been a way to replicate that, the Replicators would have taken over by now and he wouldn't exist. So he was only good for one thing: his body. Well, the genes in his body. God, he was getting punchy.

The front console sputtered to life for a moment, then died. "Try again?" he asked.

"There is a short. I must find out where."

"You do that," he said as he made his way back to his spot in the back. For some reason, he didn't want to be anywhere near the pilot's seat. He'd been shocked too many times in the last few hours sitting right there.

John found a comfortable position and closed his eyes.

* * *

"So?"

"No go. Nothing going on out there," Lorne stated as he and Ronon traveled back to Atlantis for what seemed like the fiftieth time.

Teyla turned her head, eyes wide. Lorne wished he could get into that pretty head of hers. The wisdom that she possessed had saved their asses plenty of times. It wasn't just the fact that she grew up in the Pegasus Galaxy. And it wasn't even the fact that she could kick his ass and hand it to him on a silver platter. No one gave her credit for being that damn cunning and smart.

"Which means there definitely is something going on out there," Teyla finished.

Ronon smiled. "Damn straight. We're not sure, but there's something big about to go down."

"Great. Just great. Just what we need. Another Wraith attack. Replicators? Wait, we got rid of them. Who? Can't be Michael," Rodney rattled.

Lorne watched Teyla as Rodney said the "M" word. The flinch was ever so slight, but it was there. They couldn't be sure if and when he'd ever show up. Teyla was always on guard because there was no proof that he was dead. When he had suggested Teyla go with them to search for answers to Sheppard's disappearance, Teyla had declined. Now that he didn't like.

"Whoever it is, they have people scared. No one's talking," Ronon told the group.

Lorne had seen the fear in their eyes though. Even being seen talking to the two of them could doom people or their world to destruction. The two of them had been careful as they could be, but people talk. But not to them.

"So what do we do?" Rodney inquired as they headed to Woolsey's office to give him the bad news.

"Keep looking," Lorne instructed the scientist.

"Yeah, well, needle in a haystack would be easier to find. I have a few more possibilities though," Rodney sighed. "He is so gonna pay."

Lorne admired Colonel Sheppard, even now with all the trouble that he had caused. Never leave a man behind.

* * *

"I was sleeping."

"I know. It's just, I've been a little lonely."

The hitch in her voice cut him deep. Elizabeth always seemed like she was lonely, even when there were multitudes of people in and out of her office all day long. She never had anyone to really talk to her, but he was the exception. Even when there were long hours put in, even when she was dead tired or one of them was hurting, they'd talk. If not for a few minutes, at least a few second could last for days between the two of them.

She looked so lost.

Elizabeth had curled herself into a ball, tucked into a corner of her office. He'd finally found her after searching. John had even missed her the first time he'd been in her office. She so obviously didn't want to be seen. So he'd finally given up, sat down in "his" chair and drifted off to sleep for a while. The slight movement had startled him awake. Maybe she hadn't been there before. Maybe.

"I understand."

"Do you? I never wanted any of this. You should have let me die."

John crawled over to her. The thought of trying to comfort her could never make up for what she'd been through.

"I couldn't let you die. Neither could Rodney. We thought we could deal with the nanites later."

"It didn't work."

They'd run out of time. Ultimately Elizabeth had helped them get what they needed to defeat the Replicators. But if she hadn't been infected in the first place, there was a possibility none of this would have ever happened. Just like waking up the Wraith. Oh, the possibilities.

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